Communicated by Charles D. Michener, University of Kansas, Lawrence, KS, May 16, 2006 (received for review February 2, 2006)

Bees, the largest (>16,000 species) and most important radiation of pollinating insects, originated in early to mid-Cretaceous, roughly in synchrony with the angiosperms (flowering plants). Understanding the diversification of the bees and the coevolutionary history of bees and angiosperms requires a well supported phylogeny of bees (as well as angiosperms). We reconstructed a robust phylogeny of bees at the family and subfamily levels using a data set of five genes (4,299 nucleotide sites) plus morphology (109 characters). The molecular data set included protein coding (elongation factor-1, RNA polymerase II, and LW rhodopsin), as well as ribosomal (28S and 18S) nuclear gene data. Analyses of both the DNA data set and the DNA+morphology data set by parsimony and Bayesian methods yielded a single well supported family-level tree topology that places Melittidae as a paraphyletic group at the base of the phylogeny of bees. This topology ("Melittidae-LT basal") is significantly better than a previously proposed alternative topology ("Colletidae basal") based both on likelihood and Bayesian methods. Our results have important implications for understanding the early diversification, historical biogeography, host–plant evolution, and fossil record of bees. The earliest branches of bee phylogeny include lineages that are predominantly host–plant specialists, suggesting that host–plant specificity is an ancestral trait in bees. Our results suggest an African origin for bees, because the earliest branches of the tree include predominantly African lineages. These results also help explain the predominance of Melittidae, Apidae, and Megachilidae among the earliest fossil bees.

Angiosperms (flowering plants), with an estimated 250,000–260,000 species (1), represent the largest and most diverse lineage of vascular plants on earth. To Darwin, the rapid emergence and early diversification of the angiosperms was an "abominable mystery" (ref. 2 and refs. therein). Among the most important traits attributable to the explosive radiation of the angiosperms is animal-mediated pollination (3–7). Insects are by far the most important animal pollinators (70% of angiosperm species are insect pollinated; ref. 8) and among insects, bees are the most specialized and important pollinator group. All of the >16,000 species of bees living today (9) rely virtually exclusively on angiosperm products, including pollen and nectar for adult and larval nutrition (10), floral oils for larval nutrition (11, 12), floral waxes and perfumes that serve as sexual attractants (13), and resins for nest construction (14). Bees are morphologically adapted to collecting, manipulating, carrying, and storing pollen and other plant products (15, 16), and many bee species are specialists on one or a few closely related host plants (10).

One step toward resolving Darwin's "abominable mystery" is to develop a better understanding of the role that bees played in the evolutionary history and diversification of the angiosperms. A robust phylogeny of bees would allow us to infer attributes of the early bees and to reconstruct the types of interactions that existed between the earliest bees and their angiosperm hosts. Higher-level (family- and subfamily-level) bee phylogeny is poorly understood. Currently, bees are divided into seven extant families: the long-tongued (LT) bee families Megachilidae and Apidae and the short-tongued (ST) bee families Colletidae, Stenotritidae, Andrenidae, Halictidae, and Melittidae sensu lato (s.l.)¶ (9). Colletidae is widely considered the most basal family of bees (i.e., the sister group to the rest of the bees), because all females and most males possess a glossa (tongue) with a bifid (forked) apex, much like the glossa of an apoid wasp (18–22).

However, several authors have questioned this interpretation (9, 23–27) and have hypothesized that the earliest branches of bee phylogeny may have been either Melittidae s.l., LT bees, or a monophyletic group consisting of both. The most recent morphological analysis of family-level phylogeny in bees (17) obtained two different tree topologies based on alternative coding of relatively few mouthpart characters. One tree topology places Colletidae as sister to the rest of the bees ("Colletidae basal"), whereas the other places Melittidae s.l.+LT bees as sister to the rest of the bees ("Melittidae-LT basal"). The major difference between the Colletidae basal and Melittidae-LT basal topologies involves the placement of the root node of bees (27). Placing the root between Colletidae and the rest of the bees yields the Colletidae basal topology, whereas placement of the root node near or within Melittidae s.l. yields the Melittidae-LT basal topology. The biological implications of these alternative topologies are radically different. The Colletidae basal topology implies an Australian and/or South American origin for bees and suggests the earliest bees were a mix of floral generalists and specialists. Melittidae-LT basal implies an African origin for bees and indicates that the earliest bees were likely to have been floral specialists. These alternative topologies also have implications for understanding the fossil record and antiquity of bees.

To resolve the root node of bees, we combined >4,000 bp of DNA sequence data with the previous morphological data set of Alexander and Michener (17). We report here the results of an analysis of the largest molecular and morphological study to date on bee family-level phylogeny. Our analyses provide insights into the phylogeny, historical biogeography, host–plant associations, and fossil record of bees.